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- PDB-6n5q: Structure of Human pir-miRNA-378a Apical Loop and One-base-pair F... -

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Basic information

Entry
Database: PDB / ID: 6n5q
TitleStructure of Human pir-miRNA-378a Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold
ComponentsRNA (128-MER)
KeywordsRNA / microRNA / RNA processing / Protein-RNA interaction
Function / homologyChem-2BA / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.946 Å
AuthorsShoffner, G.M. / Peng, Z. / Guo, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1616265 United States
CitationJournal: To Be Published
Title: Three-dimensional structures of pri-miRNA apical junctions and loops revealed by scaffold-directed crystallography
Authors: Shoffner, G.M. / Peng, Z. / Guo, F.
History
DepositionNov 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (128-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0919
Polymers41,5421
Non-polymers1,5498
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.850, 114.850, 114.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (128-MER)


Mass: 41541.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)

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Non-polymers , 5 types, 12 molecules

#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.25 Å3/Da / Density % sol: 76.59 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.63 M (NH4)2SO4, 0.272 M Li2SO4, and 0.1 M HEPES pH 7.4
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2017
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.946→75.131 Å / Num. obs: 18836 / % possible obs: 99.8 % / Redundancy: 19.4 % / CC1/2: 1 / Rpim(I) all: 0.015 / Rrim(I) all: 0.067 / Net I/σ(I): 25.5
Reflection shellResolution: 2.95→3.05 Å / Redundancy: 18.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1884 / CC1/2: 0.84 / Rpim(I) all: 0.346 / Rrim(I) all: 1.54 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QK8

4qk8


Resolution: 2.946→75.131 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.85
RfactorNum. reflection% reflection
Rfree0.1879 1882 9.99 %
Rwork0.165 --
obs0.1674 18836 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 330.83 Å2 / Biso mean: 117.2108 Å2 / Biso min: 51.23 Å2
Refinement stepCycle: final / Resolution: 2.946→75.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2747 98 4 2849
Biso mean--78.72 66.83 -
Num. residues----128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9456-3.02530.38411390.36481246138597
3.0253-3.11430.31391430.280112871430100
3.1143-3.21480.29541410.244512731414100
3.2148-3.32970.24171440.226212891433100
3.3297-3.4630.2071440.193812951439100
3.463-3.62060.21781420.208712911433100
3.6206-3.81150.20421430.176812901433100
3.8115-4.05030.2151460.172413151461100
4.0503-4.3630.19941430.165112891432100
4.363-4.8020.19041470.145313191466100
4.802-5.49670.15361470.142713281475100
5.4967-6.92450.18411480.146313311479100
6.9245-75.15520.14461550.13791401155699

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